A memory device, a memory system, and operating methods thereof are provided. The method of operating the memory device, which includes a first memory cell and a second memory cell neighboring the first memory cell, includes counting a disturbance value of the second memory cell each time the first memory cell is accessed, updating a disturbance count value of the second memory cell based on the counting, adjusting a refresh schedule based on the disturbance count value of the second memory cell, a desired threshold and a maximum disturbance count value, and resetting the disturbance count value of the second memory cell and the maximum disturbance count value when the second memory cell is refreshed according to the adjusted refresh schedule.